Download Using Make Fan - Filogenetica.org

MakeFan
H. David Sheets
[email protected]
This is a very rough user’s manual for MakeFan, it will eventually be replaced with
something a bit more polished. MakeFan draws “fans”, which are radial guidelines with
equal angular spacing on images (tiff, jpeg or bitmap) of specimens to aid in digitizing
points along curves or contours. This approach is intended to be used in conjunction with
semi-landmark methods, utilizing the SemiLand6 program. Obtain a copy of SemiLand6
if you haven’t already, and read the files SemiLand6_manual and Semi-Land_becki
included with it as well.
The first section of this manual is the pdf form of a PowerPoint presentation on MakeFan
I wrote for a workshop on morphometrics at Berkeley in June 2002. The comment about
the Red Wings is a joke about Miriam, ask her what it means when you meet her....
Following the Power Point derived material, is a short set of instructions on how to run
MakeFan.
Using Make Fan
What is a fan and why do I need one?
How do you use MakeFan6?
Digitizing within MakeFan6?
A fan is a graphical tool for picking out points
to digitize along a curve
A triangular Fan- the rays are evenly angularly spaced.
This is a circular fan.
Placing a fan on an image.
•Load the image into Makefan
(tiff, jpeg,bitmap)
•Place one or more fans
•Save the image with fans (as .tif)
•Digitize in TPSDig
Specifying the type and location
of a fan
•Triangular or Circular?
•End points of the fan
•Mid-point of the fan
•Length of the fan
•Line Weight
Making a Triangular Fan. Place three points:
1-left or Counter Clockwise edge,
2- the center
3-the right or Clockwise edge
3
1
2
1
m id -p o in t
2
3
For this circular fan, the mid point of a set of three
points (1,2,3) is used as the center of the fan.
1
2
It is also possible to generate a circular fine about the
midpoint of a line. The line is specified by endpoints 1,2
1
3
4
2
A fan may be drawn using the midpoint of four
markers as well.
Here’s what it looks like on an
organism.
A fish-fan.
And despite the obvious
relevance…
I was unable to come up with a
Red Wings Fan…..
Pesky Details….
•Use the File menu to load and save images.
Saved files are always tiff format.
•The “Number of Lines” controls the numbers of
lines in the fan
•The “Exaggeration” controls the line length.
An exaggeration of 1 draws from point 1
to the midpoint. Larger exaggerations
increase the line length. Experiment.
• Makefan6 can digitize points, but is not
recommended. Use TPSDig.
Still More Details…
•You can increase the line weight of the fan
using an option on the “image” menu.
•Zoom functions are also on the image menu.
Be careful when zooming, at the moment
you can foul up the aspect ratio, it can be
reset using an option on the “image”
menu.
•You can also remove a marker (point) placed
on an image by using the option in the
“image” menu.
Using the MakeFan6 image processing Tool
H. D. Sheets, August 2002,
[email protected]
1.) Expand MakeFan6 into the same directory as the rest of your IMP software, which
should be the subdirectory /bin/win32. Try starting MakeFan. If it does not load
correctly, or step 2 below fails, obtain the file EXTRADLL.EXE from the website and
expand it into the bin/win32 directory with the rest of your IMP software. I am trying to
clean this up so it isn’t such a hassle, but no luck yet.
2.) Load an image into MakeFan using the File menu on MakeFan. MakeFan will load
jpeg, tiff or bitmap (bmp). Tiff seems to be the most reliable.
3.) Place your markers (1,2,3,4) as desired to create fans. Use the different Fan options to
create different fans. Plan on spending some time experimenting with the fans to figure
out what you will need to use.
4.) When you have a fan placed, use the File option on the MakeFan window to save
TIFF, JPEG or BITMAP images with the fan on them to disk. MakeFan works with only
one image per file.
5.) If you load a new image into MakeFan it will replace the prior image.
Make Fan does have the ability to digitize landmarks, although it is not as good a
program for this as TPSDig. I haven’t written a manual for these operations of MakeFan,
but feel free to mess around with it. To start digitizing, click on the Place LM button,
then position the cursor and click to place landmarks. Each landmark will be numbered.
To stop placing landmarks, move the cursor to the far lower right of the screen (not on
the EXIT button, please) and click there, off of the image. The cross-hairs should then
shut off. The button DEL LAST LM will delete the last landmark you placed. If you hit
the place landmark button again, you can start placing landmarks on the screen again.
The landmark configuration may be saved using the SAVE TPS FILE option on the file
menu. MakeFan is not meant as a full-service digitizer, by any means….If you are
ambitious, you could do some Matlab programming to make your own customized
digitizer out of MakeFan….
The Zoom option can distort the aspect ratio on you. There is an option on the image
menu that will restore the aspect ratio to the correct value.
There are commands that will erase the markers on the image menu, if you do not want
them to appear on the saved image.